The complete nucleotide sequence of Subterranean clover mottle virus

Abstract

The complete nucleotide sequence of Subterranean clover mottle virus (SCMoV) genomic RNA has been determined. The SCMoV genome is 4,258 nucleotides in length. It shares most nucleotide and amino acid sequence identity with the genome of Lucerne transient streak virus (LTSV). SCMoV RNA encodes four overlapping open reading frames and has a genome organisation similar to that of Cocksfoot mottle virus (CfMV). ORF1 and ORF4 are predicted to encode single proteins. ORF2 is predicted to encode two proteins that are derived from a -1 translational frameshift between two overlapping reading frames (ORF2a and ORF2b). A search of amino acid databases did not find a significant match for ORF1 and the function of this protein remains unclear. ORF2a contains a motif typical of chymotrypsin-like serine proteases and ORF2b has motifs characteristically present in positive-stranded RNA-dependent RNA polymerases. ORF4 is likely to be expressed from a subgenomic RNA and encodes the viral coat protein. The ORF2a/ORF2b overlapping gene expression strategy used by SCMoV and CfMV is similar to that of the poleroviruses and differ from that of other published sobemoviruses. These results suggest that the sobemoviruses could now be divided into two distinct subgroups based on those that express the RNA-dependent RNA polymerase from a single, in-frame polyprotein, and those that express it via a -1 translational frameshifting mechanism.

Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present

“…Several isolates of Subterranean clover mottle virus (SCMoV, genus Sobemovirus ), which caused a disease restricted to southwest Australia, were fully sequenced [28]. The highest divergence between two isolates collected in 1991 and 1996, respectively, was 1.2%.…”

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

“…The most 5′ proximal ORF1 encoding protein P1 is situated in weak context for optimal translation initiation [ 47 , 48 ] and this enables pre-bound 40S ribosomes to bypass its start codon and to initiate translation from the subsequent ORF. It has been demonstrated that the deletion of the start codon of SCPMV ORF1 increased translation from downstream ORF2a/2ab, whereas mutations making SCPMV ORF1 translation initiation context more favorable reduced the downstream protein expression [ 49 ].…”

The Ryegrass mottle virus genome codes for a sobemovirus 3C-like serine protease and RNA-dependent RNA polymerase translated via −1 ribosomal frameshifting

“…Earlier multiple AA sequence alignments conducted by Dwyer et al [3] surprisingly demonstrated similarity of N-terminal part of RdRPs of CfMV-like sobemoviruses to unknown ORF3 products of SCPMV-type sobemovirus genomes, including RGMoV, RYMV, and SeMV. Similarly to our sequencing data, recently published corrected sequences of RYMV [8] and SeMV (Genbank No.AY004291) demonstrated excessive nucleotides in ORF2, which have led to wrongly interpreted genome organization in early publications [2].…”

“…For other sequenced sobemovirus genomes (CfMV, SCMoV, TRoV), a different, CfMV-type polyprotein coding strategy has been found. Instead of large polyprotein genes with nested ORF3 the genomes of these viruses contain two overlapping ORFs, and putative RdRP's are formed as a C-terminal part of polyprotein via -1 ribosomal frameshifting [2][3][4]. The latest sequencing of RYMV [8] and SeMV (Genbank No.…”

“…RGMoV ORF2a codes for protease and putative VPg (Pro-VPg). ORF2b appears to code for RdRP, which can be translated via the -1 ribosomal frameshifting mechanism at strongly conserved [1][2][3][4] sobemovirus heptanucleotide slippery sequence (UUUAAAC; nt pos. 1842-1848; Fig.…”